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Houston R, Desai S, Takayanagi A, Quynh Thu Tran C, Mortezaei A, Oladaskari A, Sourani A, Siddiqi I, Khodayari B, Ho A, Hariri O. A Multidisciplinary Update on Treatment Modalities for Metastatic Spinal Tumors with a Surgical Emphasis: A Literature Review and Evaluation of the Role of Artificial Intelligence. Cancers (Basel) 2024; 16:2800. [PMID: 39199573 PMCID: PMC11352440 DOI: 10.3390/cancers16162800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/16/2024] [Accepted: 07/29/2024] [Indexed: 09/01/2024] Open
Abstract
Spinal metastases occur in up to 40% of patients with cancer. Of these cases, 10% become symptomatic. The reported incidence of spinal metastases has increased in recent years due to innovations in imaging modalities and oncological treatments. As the incidence of spinal metastases rises, so does the demand for improved treatments and treatment algorithms, which now emphasize greater multidisciplinary collaboration and are increasingly customized per patient. Uniquely, we discuss the potential clinical applications of AI and NGS in the treatment of spinal metastases. Material and Methods: A PubMed search for articles published from 2000 to 2023 regarding spinal metastases and artificial intelligence in healthcare was completed. After screening for relevance, the key findings from each study were summarized in this update. Results: This review summarizes the evidence from studies reporting on treatment modalities for spinal metastases, including minimally invasive surgery (MIS), external beam radiation therapy (EBRT), stereotactic radiosurgery (SRS), CFR-PEEK instrumentation, radiofrequency ablation (RFA), next-generation sequencing (NGS), artificial intelligence, and predictive models.
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Affiliation(s)
- Rebecca Houston
- Department of Neurosurgery, Arrowhead Regional Medical Center, 400 N Pepper Ave, Colton, CA 92324, USA;
| | - Shivum Desai
- Department of Neurosurgery, Ascension Providence Hospital, 16001 W Nine Mile Rd, Southfield, MI 48075, USA;
| | - Ariel Takayanagi
- Department of Neurosurgery, Riverside University Health System, 26520 Cactus Ave, Moreno Valley, CA 92555, USA; (A.T.); (I.S.)
| | - Christina Quynh Thu Tran
- Kaiser Permanente Bernard J. Tyson School of Medicine, 98 S Los Robles Ave, Pasadena, CA 91101, USA;
| | - Ali Mortezaei
- Student Research Committee, Gonabad University of Medical Sciences, Gonabad 9P67+R29, Razavi Khorasan, Iran;
| | - Alireza Oladaskari
- School of Biological Sciences, University of California Irvine, 402 Physical Sciences Quad, Irvine, CA 92697, USA;
| | - Arman Sourani
- Department of Neurosurgery, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan JM76+5M3, Isfahan, Iran;
- Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Hezar Jerib Avenue, Isfahan JM76+5M3, Isfahan, Iran
| | - Imran Siddiqi
- Department of Neurosurgery, Riverside University Health System, 26520 Cactus Ave, Moreno Valley, CA 92555, USA; (A.T.); (I.S.)
| | - Behnood Khodayari
- Department of Radiation Oncology, Kaiser Permanente Los Angeles Medical Center, 4867 W Sunset Blvd, Los Angeles, CA 90027, USA;
| | - Allen Ho
- Department of Neurological Surgery, Kaiser Permanente Orange County, 3440 E La Palma Ave, Anaheim, CA 92806, USA;
| | - Omid Hariri
- Department of Neurosurgery, Arrowhead Regional Medical Center, 400 N Pepper Ave, Colton, CA 92324, USA;
- Kaiser Permanente Bernard J. Tyson School of Medicine, 98 S Los Robles Ave, Pasadena, CA 91101, USA;
- Department of Neurological Surgery, Kaiser Permanente Orange County, 3440 E La Palma Ave, Anaheim, CA 92806, USA;
- Department of Surgery, Western University of Health Sciences, 309 E 2nd St, Pomona, CA 91766, USA
- Department of Orthopedic Surgery, University of California Irvine School of Medicine, 1001 Health Sciences Rd, Irvine, CA 92617, USA
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Ahmad S, Lohiya S, Taksande A, Meshram RJ, Varma A, Vagha K. A Comprehensive Review of Innovative Paradigms in Microbial Detection and Antimicrobial Resistance: Beyond Traditional Cultural Methods. Cureus 2024; 16:e61476. [PMID: 38952583 PMCID: PMC11216122 DOI: 10.7759/cureus.61476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024] Open
Abstract
Microbial detection and antimicrobial resistance (AMR) surveillance are critical components of public health efforts to combat infectious diseases and preserve the efficacy of antimicrobial agents. While foundational in microbial identification, traditional cultural methods are often laborious, time-consuming, and limited in their ability to detect AMR markers. In response to these challenges, innovative paradigms have emerged, leveraging advances in molecular biology, genomics, proteomics, nanotechnology, and bioinformatics. This comprehensive review provides an overview of innovative approaches beyond traditional cultural methods for microbial detection and AMR surveillance. Molecular-based techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer enhanced sensitivity and specificity, enabling the rapid identification of microbial pathogens and AMR determinants. Mass spectrometry-based methods provide rapid and accurate detection of microbial biomarkers, including matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and biosensor technologies. Nanotechnology approaches, such as nanoparticle-based assays and nanopore sequencing, offer novel platforms for sensitive and label-free detection of pathogens and AMR markers. Embracing these innovative paradigms holds immense promise for improving disease diagnosis, antibiotic stewardship, and AMR containment efforts. However, challenges such as cost, standardization, and integration with existing healthcare systems must be addressed to realize the full potential of these technologies. By fostering interdisciplinary collaboration and innovation, we can strengthen our ability to detect, monitor, and combat AMR, safeguarding public health for generations.
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Affiliation(s)
- Shahzad Ahmad
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Sham Lohiya
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
- Pediatrics, Acharya Vinoba Bhave Rural Hospital, Wardha, IND
| | - Amar Taksande
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Revat J Meshram
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Ashish Varma
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Keta Vagha
- Pediatrics, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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Wakefield C, Hornick JL. Update on immunohistochemistry in bone and soft tissue tumors: Cost-effectively replacing molecular testing with immunohistochemistry. Hum Pathol 2024; 147:58-71. [PMID: 38135060 DOI: 10.1016/j.humpath.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023]
Abstract
Soft tissue tumors form part of a challenging domain in diagnostic pathology owing to their comparative rarity, astonishing histologic diversity, and overlap between entities. Many of these tumors are now known to be defined by highly recurrent, or, in some instances, unique molecular alterations. Insights from gene profiling continue to elucidate the wider molecular landscape of soft tissue tumors; many of these advances have been co-opted by immunohistochemistry (IHC) for diagnostic applications. There now exists a multitude of antibodies serving as surrogate markers of recurrent gene fusions, amplifications, and point mutations, which, in certain settings, can replace the need for more resource and time-intensive cytogenetic and molecular genetic analyses. IHC presents many advantages including rapid turnaround time, cost-effectiveness, and interpretative reproducibility. A sensible application of these immunohistochemical markers complemented by a working knowledge of the molecular pathogenesis of bone and soft tissue tumors permits accurate diagnosis in the majority of cases. In this review, we will outline some of these biomarkers while emphasizing molecular correlates and highlighting interpretative challenges and pitfalls.
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Affiliation(s)
- Craig Wakefield
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.
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Popova L, Carabetta VJ. The use of next-generation sequencing in personalized medicine. ARXIV 2024:arXiv:2403.03688v1. [PMID: 38495572 PMCID: PMC10942477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The revolutionary progress in development of next-generation sequencing (NGS) technologies has made it possible to deliver accurate genomic information in a timely manner. Over the past several years, NGS has transformed biomedical and clinical research and found its application in the field of personalized medicine. Here we discuss the rise of personalized medicine and the history of NGS. We discuss current applications and uses of NGS in medicine, including infectious diseases, oncology, genomic medicine, and dermatology. We provide a brief discussion of selected studies where NGS was used to respond to wide variety of questions in biomedical research and clinical medicine. Finally, we discuss the challenges of implementing NGS into routine clinical use.
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Affiliation(s)
- Liya Popova
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden NJ, 08103
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Wong BYL, Li Z, Raphael MJ, De Angelis C, Hwang DM, Fu L. Developing DPYD Genotyping Method for Personalized Fluoropyrimidines Therapy. J Appl Lab Med 2024; 9:295-304. [PMID: 38084968 DOI: 10.1093/jalm/jfad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/15/2023] [Indexed: 03/02/2024]
Abstract
BACKGROUND Fluoropyrimidine drugs are widely used in chemotherapy to treat solid tumors. However, severe toxicity has been reported in 10% to 40% of patients. The DPYD gene encodes the rate-limiting enzyme dihydropyrimidine dehydrogenase responsible for fluoropyrimidine catabolism. The DPYD variants resulting in decreased or no enzyme activity are associated with increased risk of fluoropyrimidine toxicity. This study aims to develop a pharmacogenetic test for screening DPYD variants to guide fluoropyrimidine therapy. METHODS A multiplex allele-specific polymerase chain reaction (AS-PCR) assay, followed by capillary electrophoresis, was developed to detect 5 common DPYD variants (c.557A > G, c.1129-5923C > G, c.1679T > G, c.1905 + 1G > A, and c.2846A > T). Deidentified population samples were used for screening positive controls and optimizing assay conditions. Proficiency testing samples with known genotypes were analyzed for test validation. All variants detected were confirmed by Sanger sequencing. RESULTS From the deidentified population samples, 5 samples were heterozygous for c.557A > G, 2 samples were heterozygous for c.1129-5923C > G (HapB3), and 1 sample was heterozygous for c.2846A > T. The 20 proficiency samples matched with their assigned genotypes, including 13 wild-type samples, 3 samples heterozygous for c.1679T > G, 2 samples heterozygous for c.1905 + 1G > A, and 2 samples heterozygous for c.2846A > T. One of the 3 patient samples was heterozygous for c.1129-5923C > G (HapB3). All the variants detected by the multiplex AS-PCR assay were concordant with Sanger sequencing results. CONCLUSIONS A robust multiplex AS-PCR assay was developed to rapidly detect 5 variants in the DPYD gene. It can be used for screening DPYD variants to identify patients with increased risk of toxicity when prescribed fluoropyrimidine therapy.
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Affiliation(s)
- Betty Y L Wong
- Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Zhenyu Li
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Michael Jonathon Raphael
- Department of Medicine, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Oncology, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Carlo De Angelis
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacy, Sunnybrook Odette Cancer Centre,Toronto, Ontario, Canada
| | - David M Hwang
- Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Lei Fu
- Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
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Chandy T. Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects. Dement Neuropsychol 2023; 17:e20220025. [PMID: 37577182 PMCID: PMC10417152 DOI: 10.1590/1980-5764-dn-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 08/15/2023] Open
Abstract
Clinical diagnosis of several neurodegenerative disorders based on clinical phenotype is challenging due to its heterogeneous nature and overlapping disease manifestations. Therefore, the identification of underlying genetic mechanisms is of paramount importance for better diagnosis and therapeutic regimens. With the emergence of next-generation sequencing, it becomes easier to identify all gene variants in the genome simultaneously, with a system-wide and unbiased approach. Presently various bioinformatics databases are maintained on discovered gene variants and phenotypic indications are available online. Since individuals are unique in their genome, evaluation based on their genetic makeup helps evolve the diagnosis, counselling, and treatment process at the personal level. This article aims to briefly summarize the utilization of next-generation sequencing in deciphering the genetic causes of Alzheimer's disease and address the limitations of whole genome and exome sequencing.
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Affiliation(s)
- Tijimol Chandy
- MedGenome Labs Pvt. Ltd., Bangalore-560100, Karnataka, India
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Lau-Min KS, McCarthy AM, Nathanson KL, Domchek SM. Nationwide Trends and Determinants of Germline BRCA1/2 Testing in Patients With Breast and Ovarian Cancer. J Natl Compr Canc Netw 2023; 21:351-358.e4. [PMID: 37015340 PMCID: PMC10256435 DOI: 10.6004/jnccn.2022.7257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/21/2022] [Indexed: 04/06/2023]
Abstract
BACKGROUND Germline genetic testing (GT) for BRCA1/2 is instrumental in identifying patients with breast and ovarian cancers who are eligible for PARP inhibitors (PARPi). Little is known about recent trends and determinants of GT since PARPi were approved for these patients. PATIENTS AND METHODS We performed a retrospective cohort study of patients in a nationwide electronic health record (EHR)-derived oncology-specific database with the following GT eligibility criteria: breast cancer diagnosed at age ≤45 years, triple-negative breast cancer diagnosed at age ≤60 years, male breast cancer, or ovarian cancer. GT within 1 year of diagnosis was assessed and stratified by tumor type. Multivariable log-binomial regressions estimated adjusted relative risks (RRs) of GT by patient and tumor characteristics. RESULTS Among 2,982 eligible patients with breast cancer, 56.4% underwent GT between January 2011 and March 2020, with a significant increase in GT over time (RR, 1.08; 95% CI, 1.05-1.11, for each year), independent of when PARPi were approved for BRCA1/2-mutated metastatic breast cancer in January 2018. In multivariable analyses, older age (RR, 0.93; 95% CI, 0.90-0.96, for every 5 years) and Medicare coverage (RR, 0.69; 95% CI, 0.49-0.96 vs commercial insurance) were associated with less GT. Among 5,563 eligible patients with ovarian cancer, 35.4% underwent GT between January 2011 and March 2020, with a significant increase in GT over time (RR, 1.11; 95% CI, 1.07-1.14, for each year) that accelerated after approval of PARPi for BRCA1/2-mutated, chemotherapy-refractory ovarian cancer in December 2014 (RR, 1.42; 95% CI, 1.19-1.70). Older age (RR, 0.95; 95% CI, 0.93-0.97, for every 5 years) and Black or African American race (RR, 0.80; 95% CI, 0.65-0.98 vs White race) were associated with less GT. CONCLUSIONS GT remains underutilized nationwide among patients with breast and ovarian cancers. Although GT has increased over time, significant disparities by age, race, and insurance status persist. Additional work is needed to design, implement, and evaluate strategies to ensure that all eligible patients receive GT.
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Affiliation(s)
- Kelsey S. Lau-Min
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School
| | - Anne Marie McCarthy
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Katherine L. Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
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Lee S, Hong S, Park J, Koh Y, Lee H, Yang J, Seo SW, Kim SJ. dCas9-Mediated PCR-Free Detection of Oncogenic Mutation by Nonequilibrium Nanoelectrokinetic Selective Preconcentration. Anal Chem 2023; 95:5045-5052. [PMID: 36893461 DOI: 10.1021/acs.analchem.2c05539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Cutting-edge nanoelectrokinetic technology in this work provides a breakthrough for the present clinical demands of molecular diagnosis to detect a trace amount of oncogenic mutation of DNA in a short time without an erroneous PCR procedure. In this work, we combined the sequence-specific labeling scheme of CRISPR/dCas9 and ion concentration polarization (ICP) mechanism to separately preconcentrate target DNA molecules for rapid detection. Using the mobility shift caused by dCas9's specific binding to the mutant, the mutated DNA and normal DNA were distinguished in the microchip. Based on this technique, we successfully demonstrated the dCas9-mediated 1-min detection of single base substitution (SBS) in EGFR DNA, a carcinogenesis indicator. Moreover, the presence/absence of target DNA was identified at a glance like a commercial pregnancy test kit (two lines for positive and one line for negative) by the distinct preconcentration mechanisms of ICP, even at the 0.1% concentration of the target mutant.
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Affiliation(s)
- Sangjun Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seongjun Hong
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihee Park
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Hyomin Lee
- Department of Chemical and Biological Engineering, Jeju National University, Jeju 63243, Republic of Korea
| | - Jina Yang
- Department of Chemical and Biological Engineering, Jeju National University, Jeju 63243, Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Jae Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
- SOFT Foundry Institute, Seoul National University, Seoul 08826, Republic of Korea
- Inter-university Semiconductor Research Center, Seoul National University, Seoul 08826, Republic of Korea
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Treichel AM, Boeszoermenyi B, Lee CCR, Moss J, Kwiatkowski DJ, Darling TN. Diagnosis of Mosaic Tuberous Sclerosis Complex Using Next-Generation Sequencing of Subtle or Unusual Cutaneous Findings. JID INNOVATIONS 2023; 3:100180. [PMID: 36960317 PMCID: PMC10030254 DOI: 10.1016/j.xjidi.2023.100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 01/11/2023] Open
Abstract
Skin findings can be critical to determining whether a patient with lymphangioleiomyomatosis (LAM), a progressive pulmonary disease that predominantly affects adult women, has sporadic LAM or LAM in association with tuberous sclerosis complex (TSC). Three individuals with LAM underwent evaluation for TSC-associated mucocutaneous and internal findings. We used our previously published algorithm to confirm the clinical suspicion for mosaicism and guide the selection of tissue specimens and genetic workup. Next-generation sequencing of cutaneous findings was used to confirm clinical suspicion for mosaic TSC in individuals with LAM. Two individuals previously thought to have sporadic LAM were diagnosed with mosaic TSC-associated LAM upon next-generation sequencing of unilateral angiofibromas in one and an unusual cutaneous hamartoma in the other. A third individual, diagnosed with TSC in childhood, was found to have a mosaic pathogenic variant in TSC2 in cutaneous tissue from a digit with macrodactyly. Accurate diagnosis of mosaic TSC-associated LAM may require enhanced genetic testing and is important because of the implications regarding surveillance, prognosis, and risk of transmission to offspring.
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Affiliation(s)
- Alison M. Treichel
- Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Barbara Boeszoermenyi
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Chyi-Chia Richard Lee
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David J. Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas N. Darling
- Department of Dermatology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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Abstract
Knowledge of an underlying genetic predisposition to cancer allows the use of personalised prognostic, preventive and therapeutic strategies for the patient and carries clinical implications for family members. Despite great progress, we identified six challenging areas in the management of patients with hereditary cancer predisposition syndromes and suggest recommendations to aid in their resolution. These include the potential for finding unexpected germline variants through somatic tumour testing, optimal risk management of patients with hereditary conditions involving moderate-penetrance genes, role of polygenic risk score in an under-represented Asian population, management of variants of uncertain significance, clinical trials in patients with germline pathogenic variants and technology in genetic counselling. Addressing these barriers will aid the next step forward in precision medicine in Singapore. All stakeholders in healthcare should be empowered with genetic knowledge to fully leverage the potential of novel genomic insights and implement them to provide better care for our patients.
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Affiliation(s)
- Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore
| | - Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore,Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore,Correspondence: A/Prof. Joanne Ngeow, Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Drive, 308232, Singapore. E-mail:
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Boppudi SM, Scheil-Bertram S, Faust E, Annamneedi A, Fisseler-Eckhoff A. Assessing and Evaluating the Scope and Constraints of Idylla Molecular Assays by Using Different Source Materials in Routine Diagnostic Settings. Int J Mol Sci 2022; 23:ijms232012515. [PMID: 36293374 PMCID: PMC9604085 DOI: 10.3390/ijms232012515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
For cancer treatment, diagnostics concerning tumor type and determination of molecular markers in short TAT is critical. The fully automated, real-time PCR-based molecular diagnostic Idylla assays are well established in many laboratories for qualitative detection, short TAT and routine screening of clinically relevant oncogenic mutations. According to the manufacturer, all IVD assays are recommended for use only with FFPE tissue samples of 5–10 µM dissections with at least 10% tumor content. In this study, we tested the performance and accuracy of the IVD assays along with the gene fusion assay (RUO) with different tissue/source materials like isolated DNA/RNA, cryomaterial, etc. The study also included testing archival FFPE tissue sections dating back from 20 years and a performance check for different pan-cancer samples individually. All the assays tested with FFPE sections and gDNA/RNA input showed above 96% accuracy and sensitivity, individually with 100% specificity. The Idylla assays also performed exceptionally well on the archival FFPE tissues, and the use of assays for other solid tumors was also remarkable. The performance test and accuracy of Idylla assays showed high efficiency with certain limitations. For the use of Idylla assays, both qualitative and quantitative applicability of different tumor source materials could produce efficient results in different diagnostic settings within a short TAT.
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Affiliation(s)
- Sanga Mitra Boppudi
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
- Gemeinschaftspraxis für Pathologie, 65199 Wiesbaden, Germany
- Correspondence: (S.M.B.); (A.F.-E.)
| | - Stefanie Scheil-Bertram
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
| | - Elisabeth Faust
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
| | - Anil Annamneedi
- Team Biology of GPCR Signaling Systems (BIOS), CNRS, IFCE, INRAE, Université de Tours, Physiologie de la Reproduction et des Comportements (PRC), 37380 Nouzilly, France
- LE STUDIUM Loire Valley Institute for Advanced Studies, 45000 Orléans, France
| | - Annette Fisseler-Eckhoff
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
- Gemeinschaftspraxis für Pathologie, 65199 Wiesbaden, Germany
- Correspondence: (S.M.B.); (A.F.-E.)
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Buszka K, Ntzifa A, Owecka B, Kamińska P, Kolecka-Bednarczyk A, Zabel M, Nowicki M, Lianidou E, Budna-Tukan J. Liquid Biopsy Analysis as a Tool for TKI-Based Treatment in Non-Small Cell Lung Cancer. Cells 2022; 11:2871. [PMID: 36139444 PMCID: PMC9497234 DOI: 10.3390/cells11182871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 12/03/2022] Open
Abstract
The treatment of non-small cell lung cancer (NSCLC) has recently evolved with the introduction of targeted therapy based on the use of tyrosine kinase inhibitors (TKIs) in patients with certain gene alterations, including EGFR, ALK, ROS1, BRAF, and MET genes. Molecular targeted therapy based on TKIs has improved clinical outcomes in a large number of NSCLC patients with advanced disease, enabling significantly longer progression-free survival (PFS). Liquid biopsy is an increasingly popular diagnostic tool for treating TKI-based NSCLC. The studies presented in this article show that detection and analysis based on liquid biopsy elements such as circulating tumor cells (CTCs), cell-free DNA (cfDNA), exosomes, and/or tumor-educated platelets (TEPs) can contribute to the appropriate selection and monitoring of targeted therapy in NSCLC patients as complementary to invasive tissue biopsy. The detection of these elements, combined with their molecular analysis (using, e.g., digital PCR (dPCR), next generation sequencing (NGS), shallow whole genome sequencing (sWGS)), enables the detection of mutations, which are required for the TKI treatment. Despite such promising results obtained by many research teams, it is still necessary to carry out prospective studies on a larger group of patients in order to validate these methods before their application in clinical practice.
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Affiliation(s)
- Karolina Buszka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Aliki Ntzifa
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Barbara Owecka
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Paula Kamińska
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Agata Kolecka-Bednarczyk
- Department of Immunology, Chair of Pathomorphology and Clinical Immunology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Maciej Zabel
- Division of Anatomy and Histology, University of Zielona Góra, 65-046 Zielona Góra, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Evi Lianidou
- Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Joanna Budna-Tukan
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
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13
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Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors. Cancers (Basel) 2022; 14:cancers14102457. [PMID: 35626061 PMCID: PMC9139650 DOI: 10.3390/cancers14102457] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
The use of targeted Next Generation Sequencing (NGS) for the diagnostic screening of somatic variants in solid tumor samples has proven its high clinical value. Because of the large number of ongoing clinical trials for a multitude of variants in a growing number of genes, as well as the detection of proven and emerging pan-cancer biomarkers including microsatellite instability (MSI) and tumor mutation burden (TMB), the currently employed diagnostic gene panels will become vastly insufficient in the near future. Here, we describe the validation and implementation of the hybrid capture-based comprehensive TruSight Oncology (TSO500) assay that is able to detect single-nucleotide variants (SNVs) and subtle deletions and insertions (indels) in 523 tumor-associated genes, copy-number variants (CNVs) of 69 genes, fusions with 55 cancer driver genes, and MSI and TMB. Extensive validation of the TSO500 assay was performed on DNA or RNA from 170 clinical samples with neoplastic content down to 10%, using multiple tissue and specimen types. Starting with 80 ng DNA and 40 ng RNA extracted from formalin-fixed and paraffine-embedded (FFPE) samples revealed a precision and accuracy >99% for all variant types. The analytical sensitivity and specificity were at least 99% for SNVs, indels, CNVs, MSI, and gene rearrangements. For TMB, only values around the threshold could yield a deviating outcome. The limit-of-detection for SNVs and indels was well below the set threshold of 5% variant allele frequency (VAF). This validated comprehensive genomic profiling assay was then used to screen 624 diagnostic samples, and its success rate for adoption in a clinical diagnostic setting of broad solid tumor screening was assessed on this cohort.
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14
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Ettinger DS, Wood DE, Aisner DL, Akerley W, Bauman JR, Bharat A, Bruno DS, Chang JY, Chirieac LR, D'Amico TA, DeCamp M, Dilling TJ, Dowell J, Gettinger S, Grotz TE, Gubens MA, Hegde A, Lackner RP, Lanuti M, Lin J, Loo BW, Lovly CM, Maldonado F, Massarelli E, Morgensztern D, Ng T, Otterson GA, Pacheco JM, Patel SP, Riely GJ, Riess J, Schild SE, Shapiro TA, Singh AP, Stevenson J, Tam A, Tanvetyanon T, Yanagawa J, Yang SC, Yau E, Gregory K, Hughes M. Non-Small Cell Lung Cancer, Version 3.2022, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw 2022; 20:497-530. [PMID: 35545176 DOI: 10.6004/jnccn.2022.0025] [Citation(s) in RCA: 589] [Impact Index Per Article: 294.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Non-Small Cell Lung Cancer (NSCLC) provide recommended management for patients with NSCLC, including diagnosis, primary treatment, surveillance for relapse, and subsequent treatment. Patients with metastatic lung cancer who are eligible for targeted therapies or immunotherapies are now surviving longer. This selection from the NCCN Guidelines for NSCLC focuses on targeted therapies for patients with metastatic NSCLC and actionable mutations.
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Affiliation(s)
| | - Douglas E Wood
- 2Fred Hutchinson Cancer Research Center/Seattle Cancer Care Alliance
| | | | | | | | - Ankit Bharat
- 6Robert H. Lurie Comprehensive Cancer Center of Northwestern University
| | - Debora S Bruno
- 7Case Comprehensive Cancer Center/University Hospitals Seidman Cancer Center and Cleveland Clinic Taussig Cancer Institute
| | - Joe Y Chang
- 8The University of Texas MD Anderson Cancer Center
| | | | | | | | | | | | | | | | | | | | | | | | - Jules Lin
- 20University of Michigan Rogel Cancer Center
| | | | | | | | | | - Daniel Morgensztern
- 24Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine
| | - Thomas Ng
- 25The University of Tennessee Health Science Center
| | - Gregory A Otterson
- 26The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
| | | | | | | | | | | | | | - Aditi P Singh
- 30Abramson Cancer Center at the University of Pennsylvania
| | - James Stevenson
- 7Case Comprehensive Cancer Center/University Hospitals Seidman Cancer Center and Cleveland Clinic Taussig Cancer Institute
| | - Alda Tam
- 8The University of Texas MD Anderson Cancer Center
| | | | | | - Stephen C Yang
- 1The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
| | - Edwin Yau
- 32Roswell Park Comprehensive Cancer Center; and
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15
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Fan L, Yin P, Xu Z. The genetic basis of sudden death in young people - Cardiac and non-cardiac. Gene 2022; 810:146067. [PMID: 34843881 DOI: 10.1016/j.gene.2021.146067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/25/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Sudden death is one of the major causes of death in young adults. Sudden death could be a result from both genetic and environmental or acquired factors. Understanding the genetic etiology is crucial to prevent preventable sudden death for those who are not aware of their genetic condition. In fact, the spectrum of causes of sudden death is complex and varied. In this study, we reviewed the genes that are associated with multiple causes of sudden death in terms of both sudden cardiac death and sudden noncardiac death. A summary of genetic risk factors of the major causes of genetic relevant sudden death is also provided. We believe this review could benefit the researchers who are interested in sudden death genetic studies or the young people who are concerning about their own risk on sudden death.
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Affiliation(s)
- Li Fan
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200011, China
| | - Ping Yin
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200011, China
| | - Zuojun Xu
- Department of Cardiology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200011, China.
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16
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Cahaney C, Dhir A, Ghosh T. Role of Precision Medicine in Pediatric Oncology. Pediatr Ann 2022; 51:e8-e14. [PMID: 35020508 DOI: 10.3928/19382359-20211209-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Childhood cancer is the leading cause of nonaccidental death in children and adolescents. Over the past 50 years, development of novel therapies and improvements in supportive care have led to improvements in long-term survival rates. However, there remains great morbidity associated with cancer treatment among childhood cancer survivors, and the outcomes for patients who relapse remain poor. The introduction of precision medicine, an approach that uses the understanding of genetic and biochemical profiles of a disease (as enabled by next-generation sequencing) to tailor treatment to a patient, has quickly started to change the diagnostic and therapeutic landscape of pediatric oncology. With its use, a better understanding of tumor biology, improved classification systems for various cancers, and genetically and molecularly targeted therapeutic strategies have been developed. We review the implementation of precision medicine in pediatric oncology and its effect on diagnosis, management, and treatment of pediatric cancers. [Pediatr Ann. 2022;51(1):e8-e14.].
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17
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Primary Signet Ring Cell/Histiocytoid Carcinoma of the Eyelid: Clinicopathologic Analysis with Evaluation of the E-Cadherin/ β-Catenin Complex and Associated Genetic Alterations. Case Rep Pathol 2021; 2021:6628150. [PMID: 34804623 PMCID: PMC8601830 DOI: 10.1155/2021/6628150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/15/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
Signet Ring Cell (SRC)/Histiocytoid carcinoma of the eyelid is a rare neoplasm that shares histological and immunohistochemical similarities with diffuse gastric cancer and breast lobular carcinoma. The CDH1 gene, which encodes the E-cadherin protein, is the best known gene associated with these tumors. The structural and functional integrity of E-cadherin is regulated by interconnecting molecular pathways which might participate in the development of this disease. Hence, we analyzed the protein expression in key genes in E-cadherin-related pathways associated with primary SRC/Histiocytoid carcinoma of the eyelid. SRC/Histiocytoid carcinoma diagnosed in the eyelid/orbit at MD Anderson Cancer Center from 1990 to 2016 were evaluated. Clinicopathologic findings were studied to confirm the primary site of origin. Immunohistochemical studies for the expression of E-cadherin, β-catenin, c-Myc, Cyclin D1, Src, and p53 were analyzed. Next generation sequencing for the detection of somatic mutations was performed on each tumor with matched normal tissue, examining 50 cancer-related genes. Four primary SRC/Histiocytoid carcinomas of the eyelid were diagnosed in four male patients aged 40-82 years. Immunohistochemically, two tumors with loss of E-cadherin expression had weak β-catenin and low cytoplasmic staining for Src while the other two cases with intact E-cadherin showed strong β-catenin expression and high cytoplasmic expression for Src. Cyclin D1 was focally positive in three cases. Somatic mutations in CDH1, PIK3CA, and TP53 genes were detected in two cases. Our results suggest an abnormality in the convergence of E-cadherin/β-catenin pathways which may promote tumorigenesis by inducing expression of oncogenes such as Cyclin D1 and C-Myc. Mutations in CDH1, PIK3CA, and TP53 genes could induce E-cadherin dysfunction which takes part in the development and progression of this malignancy.
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18
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Yang X, Liao M, Zhang H, Gong J, Yang F, Xu M, Tremblay PL, Zhang T. An electrochemiluminescence resonance energy transfer biosensor for the detection of circulating tumor DNA from blood plasma. iScience 2021; 24:103019. [PMID: 34522862 PMCID: PMC8426273 DOI: 10.1016/j.isci.2021.103019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/02/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
A liquid biopsy is a noninvasive approach for detecting double-stranded circulating tumor DNA (ctDNA) of 90-320 nucleotides in blood plasma from patients with cancer. Most techniques employed for ctDNA detection are time consuming and require expensive DNA purification kits. Electrochemiluminescence resonance energy transfer (ECL-RET) biosensors exhibit high sensitivity, a wide response range, and are promising for straightforward sensing applications. Until now, ECL-RET biosensors have been designed for sensing short single-stranded oligonucleotides of less than 45 nucleotides. In this work, an ECL-RET biosensor comprising graphitic carbon nitride quantum dots was assessed for the amplification-free detection in the blood plasma of DNA molecules coding for the EGFR L858R mutation, which is associated with non-small-cell lung cancer. Following a low-cost pre-treatment, the highly specific ECL-RET biosensor quantified double-stranded EGFR L858R DNA of 159 nucleotides diluted into the blood within a linear range of 0.01 fM to 1 pM, demonstrating its potential for noninvasive biopsies.
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Affiliation(s)
- Xidong Yang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
| | - Meiyan Liao
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hanfei Zhang
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - JinBo Gong
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Fan Yang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Mengying Xu
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing 312300, PR China
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
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19
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Nair SV, Madhulaxmi, Thomas G, Ankathil R. Next-Generation Sequencing in Cancer. J Maxillofac Oral Surg 2021; 20:340-344. [PMID: 34408360 DOI: 10.1007/s12663-020-01462-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Objective In this article, we provide a gestalt idea about NGS technologies and their applications in cancer research and molecular diagnosis. Background Next-generation sequencing (NGS) advancements like DNA sequencing and RNA sequencing allow uncovering of genomic, transcriptomic, and epigenomic scenes of individual malignant growths. An assortment of genomic abnormalities can be screened at the same time, for example common and uncommon variations, auxiliary variations like insertions and deletions, copy-number variation, and fusion transcripts. Conclusion NGS innovations together with bioinformatics investigation, which extend our insight, are progressively used to analyze multiple genes in a cost-effective way and have been applied in examining clinical cancer samples and offering NGS-based molecular diagnosis. Application NGS is progressively significant as a device for the diagnosis of cancers.
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Affiliation(s)
- S Vinod Nair
- Department of Oral and Maxillofacial Surgery, P.M.S Dental College, Vattapara, Trivandrum, India
| | - Madhulaxmi
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College, Chennai, India
| | - Gigi Thomas
- Community Medicine, Regional Cancer Centre, Trivandrum, India
| | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, George Town, Malaysia
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20
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Macías M, Cañada-Higueras E, Alegre E, Bielsa A, Gracia J, Patiño-García A, Ferrer-Costa R, Sendino T, Andueza MP, Mateos B, Rodríguez J, Corral J, Gúrpide A, Lopez-Picazo JM, Perez-Gracia JL, Gil-Bazo I, Alkorta-Aranburu G, González Á. Performance comparison of two next-generation sequencing panels to detect actionable mutations in cell-free DNA in cancer patients. Clin Chem Lab Med 2021; 58:1341-1348. [PMID: 32623849 DOI: 10.1515/cclm-2019-1267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023]
Abstract
Background Genomic alterations studies in cell-free DNA (cfDNA) have increasing clinical use in oncology. Next-generation sequencing (NGS) technology provides the most complete mutational analysis, but nowadays limited data are available related to the comparison of results reported by different platforms. Here we compare two NGS panels for cfDNA: Oncomine™ Pan-Cancer Cell-Free Assay (Thermo Fisher Scientific), suitable for clinical laboratories, and Guardant360® (GuardantHealth), with more genes targeted but only available in an outsourcing laboratory. Methods Peripheral blood was obtained from 16 advanced cancer patients in which Guardant360® (G360) was requested as part of their clinical assistance. Blood samples were sent to be analyzed with G360 panel, and an additional blood sample was drawn to obtain and analyze cfDNA with Oncomine™ Pan-Cancer (OM) panel in an Ion GeneStudio S5™ System. Results cfDNA analysis globally rendered 101 mutations. Regarding the 55/101 mutations claimed to be included by manufacturers in both panels, 17 mutations were reported only by G360, 10 only by OM and 28 by both. In those coincident cases, there was a high correlation between the variant allele fractions (VAFs) calculated with each panel (r = 0.979, p < 0.01). Regarding the six actionable mutations with an FDA-approved therapy reported by G360, one was missed with OM. Also, 12 mutations with clinical trials available were reported by G360 but not by OM. Conclusions In summary, G360 and OM can produce different mutational profile in the same sample, even in genes included in both panels, which is especially important if these mutations are potentially druggable.
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Affiliation(s)
- Mónica Macías
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Estibaliz Alegre
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Arancha Bielsa
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Javier Gracia
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Ana Patiño-García
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Roser Ferrer-Costa
- Department of Biochemistry, Hospital Universitari Vall D'Hebron, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Teresa Sendino
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - María P Andueza
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Beatriz Mateos
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - Javier Rodríguez
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jesús Corral
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Alfonso Gúrpide
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - José M Lopez-Picazo
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jose L Perez-Gracia
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Gil-Bazo
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Program of Solid Tumors, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Álvaro González
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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21
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Park S, Lee C, Ku BM, Kim M, Park WY, Kim NKD, Ahn MJ. Paired analysis of tumor mutation burden calculated by targeted deep sequencing panel and whole exome sequencing in non-small cell lung cancer. BMB Rep 2021. [PMID: 34154699 PMCID: PMC8328823 DOI: 10.5483/bmbrep.2021.54.7.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Owing to rapid advancements in NGS (next generation sequen-cing), genomic alteration is now considered an essential pre-dictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was con-sidered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly com-pared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture re-gion, which might lead to different values of TMB; the evalu-ation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evalu-ated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R2 = 0.887). This was also reflected in clinical samples (n = 100), which showed R2 of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.
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Affiliation(s)
- Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Chung Lee
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Bo Mi Ku
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Minjae Kim
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Woong-Yang Park
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Nayoung K. D. Kim
- Geninus Inc., Seoul 05836, 3Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
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22
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Imaoka H, Sasaki M, Hashimoto Y, Watanabe K, Miyazawa S, Shibuki T, Mitsunaga S, Ikeda M. Impact of Endoscopic Ultrasound-Guided Tissue Acquisition on Decision-Making in Precision Medicine for Pancreatic Cancer: Beyond Diagnosis. Diagnostics (Basel) 2021; 11:1195. [PMID: 34209310 PMCID: PMC8307595 DOI: 10.3390/diagnostics11071195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Precision medicine in cancer treatment refers to targeted therapy based on the evaluation of biomarkers. Although precision medicine for pancreatic cancer (PC) remains challenging, novel biomarker-based therapies, such as pembrolizumab, olaparib, and entrectinib, have been emerging. Most commonly, endoscopic ultrasound-guided tissue acquisition (EUS-TA) had been used for the diagnosis of PC until now. However, advances in EUS-TA devices and biomarker testing, especially next-generation sequencing, have opened up the possibility of sequencing of various genes even in limited amounts of tissue samples obtained by EUS-TA, and identifying potential genetic alterations as therapeutic targets. Precision medicine benefits only a small population of patients with PC, but biomarker-based therapy has shown promising results in patients who once had no treatment options. Now, the role of EUS-TA has extended beyond diagnosis into decision-making regarding the treatment of PC. In this review, we mainly discuss tissue sampling by EUS-TA for biomarker testing and the current status of precision medicine for PC.
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Affiliation(s)
- Hiroshi Imaoka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa 277-8577, Chiba, Japan; (M.S.); (Y.H.); (K.W.); (S.M.); (T.S.); (S.M.); (M.I.)
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23
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Fu Y, Wang A, Zhou J, Feng W, Shi M, Xu X, Zhao H, Cai L, Feng J, Lv X, Zhang X, Xu W, Zhang Z, Ma G, Wang J, Zhou T, Zhao D, Fang H, Liu Z, Huang JA. Advanced NSCLC Patients With EGFR T790M Harboring TP53 R273C or KRAS G12V Cannot Benefit From Osimertinib Based on a Clinical Multicentre Study by Tissue and Liquid Biopsy. Front Oncol 2021; 11:621992. [PMID: 33718183 PMCID: PMC7943858 DOI: 10.3389/fonc.2021.621992] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) patients treated with first-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) almost always acquire resistance, and the development of novel techniques analyzing circulating tumor DNA (ctDNA) have made it possible for liquid biopsy to detect genetic alterations from limited amount of DNA with less invasiveness. While a large amount of patients with EGFR exon 21 p.Thr790 Met (T790M) benefited from osimertinib treatment, acquired resistance to osimertinb has subsequently become a growing challenge. Methods We performed tissue and liquid rebiopsy on 50 patients with EGFR-mutant NSCLC who acquired resistance to first-generation EGFR-TKIs. Plasma samples underwent droplet digital PCR (ddPCR) and next-generation sequencing (NGS) examinations. Corresponding tissue samples underwent NGS and Cobas® EGFR Mutation Test v2 (Cobas) examinations. Results Of the 50 patients evaluated, the mutation detection rates of liquid biopsy group and tissue biopsy group demonstrated no significant differences (41/48, 85.4% vs. 44/48, 91.7%; OR=0.53, 95% CI=0.15 to 1.95). Overall concordance, defined as the proportion of patients for whom at least one identical genomic alteration was identified in both tissue and plasma, was 78.3% (36/46, 95% CI=0.39 to 2.69). Moreover, our results showed that almost half of the patients (46%, 23/50) resistant to first-generation EGFR-TKI harbored p.Thr790 Met (T790M) mutation. 82.6% (19/23) of the T790M positive patients were analyzed by liquid biopsy and 60.9% (14/23) by tumor tissue sequencing. Meanwhile, a wide range of uncommon mutations was detected, and novel mechanisms of osimertinib resistance were discovered. In addition, 16.7% (2/12) of the T790M positive patients with either TP53 R237C or KRAS G12V failed to benefit from the subsequent osimertinib treatment. Conclusion Our results emphasized that liquid biopsy is applicable to analyze the drug resistance mechanisms of NSCLC patients treated with EGFR-TKIs. Moreover, we discovered two uncommon mutations, TP53 R273C and KRAS G12V, which attenuates the effectiveness of osimertinib.
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Affiliation(s)
- Yulong Fu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China
| | - Anqi Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China
| | - Jieqi Zhou
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China
| | - Wei Feng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Minhua Shi
- Department of Respiratory Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiao Xu
- Department of Respiratory Medicine, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Hongqing Zhao
- Department of Respirology, Nanjing Medical University Affiliated Wuxi Second Hospital, Wuxi, China
| | - Liming Cai
- Department of Respiratory Medicine, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jian Feng
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xuedong Lv
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaodong Zhang
- Department of Medical Oncology, Nantong Tumor Hospital, Nantong, China
| | - Wenjing Xu
- Departments of Respiratory Medicine, Northern Jiangsu People's Hospital, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Zhengrong Zhang
- Department of Respiratory Medicine, First People's Hospital of Yangzhou City, Yangzhou, China
| | - Guoer Ma
- Department of Respiratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Jian Wang
- Department of Respiratory Medicine, Zhenjiang First People's Hospital, Zhenjiang, China
| | - Tong Zhou
- Department of Oncology, Changzhou Cancer Hospital Affiliated to Soochow University, Changzhou, China
| | - Dahai Zhao
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Anhui Medical University, Hefei, China
| | - Haohui Fang
- Department of Respiratory Medicine, Anhui Chest Hospital, Hefei, China
| | - Zeyi Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China.,Institute of Respiratory Diseases, Soochow University, Suzhou, China
| | - Jian-An Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China.,Suzhou Key Laboratory for Respiratory Diseases, Suzhou, China.,Institute of Respiratory Diseases, Soochow University, Suzhou, China
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Prasad A, Bhargava H, Gupta A, Shukla N, Rajagopal S, Gupta S, Sharma A, Valadi J, Nigam V, Suravajhala P. Next Generation Sequencing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Sandmann S, Wöste M, de Graaf AO, Burkhardt B, Jansen JH, Dugas M. CopyDetective: Detection threshold-aware copy number variant calling in whole-exome sequencing data. Gigascience 2020; 9:giaa118. [PMID: 33135740 PMCID: PMC7604644 DOI: 10.1093/gigascience/giaa118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/17/2020] [Accepted: 10/02/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Copy number variants (CNVs) are known to play an important role in the development and progression of several diseases. However, detection of CNVs with whole-exome sequencing (WES) experiments is challenging. Usually, additional experiments have to be performed. FINDINGS We developed a novel algorithm for somatic CNV calling in matched WES data called "CopyDetective". Different from other approaches, CNV calling with CopyDetective consists of a 2-step procedure: first, quality analysis is performed, determining individual detection thresholds for every sample. Second, actual CNV calling on the basis of the previously determined thresholds is performed. Our algorithm evaluates the change in variant allele frequency of polymorphisms and reports the fraction of affected cells for every CNV. Analyzing 4 WES data sets (n = 100) we observed superior performance of CopyDetective compared with ExomeCNV, VarScan2, ControlFREEC, ExomeDepth, and CNV-seq. CONCLUSIONS Individual detection thresholds reveal that not every WES data set is equally apt for CNV calling. Initial quality analyses, determining individual detection thresholds-as realized by CopyDetective-can and should be performed prior to actual variant calling.
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Affiliation(s)
- Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Building A11, Münster 48149, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Building A11, Münster 48149, Germany
| | - Aniek O de Graaf
- Laboratory Hematology, RadboudUMC, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, Netherlands
| | - Birgit Burkhardt
- Paediatric Hematology & Oncology, University Hospital Münster, Albert-Schweitzer-Campus 1, Building A1, Münster 48149, Germany
| | - Joop H Jansen
- Laboratory Hematology, RadboudUMC, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, Netherlands
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, Building A11, Münster 48149, Germany
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26
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Grigoriadou GΙ, Esagian SM, Ryu HS, Nikas IP. Molecular Profiling of Malignant Pleural Effusions with Next Generation Sequencing (NGS): Evidence that Supports Its Role in Cancer Management. J Pers Med 2020; 10:jpm10040206. [PMID: 33139621 PMCID: PMC7712846 DOI: 10.3390/jpm10040206] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Malignant pleural effusions (MPEs) often develop in advanced cancer patients and confer significant morbidity and mortality. In this review, we evaluated whether molecular profiling of MPEs with next generation sequencing (NGS) could have a role in cancer management, focusing on lung cancer. We reviewed and compared the diagnostic performance of pleural fluid liquid biopsy with other types of samples. When applied in MPEs, NGS may have comparable performance with corresponding tissue biopsies, yield higher DNA amount, and detect more genetic aberrations than blood-derived liquid biopsies. NGS in MPEs may also be preferable to plasma liquid biopsy in advanced cancer patients with a MPE and a paucicellular or it could be difficult to obtain tissue/fine-needle aspiration biopsy. Of interest, post-centrifuge supernatant NGS may exhibit superior results compared to cell pellet, cell block or other materials. NGS in MPEs can also guide clinicians in tailoring established therapies and identifying therapy resistance. Evidence is still premature regarding the role of NGS in MPEs from patients with cancers other than lung. We concluded that MPE processing could provide useful prognostic and theranostic information, besides its diagnostic role.
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Affiliation(s)
- Georgia Ι. Grigoriadou
- 1st Department of Medical Oncology, Theageneio Anticancer Hospital, 54007 Thessaloniki, Greece;
| | - Stepan M. Esagian
- Department of Medicine, School of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul 03080, Korea;
| | - Ilias P. Nikas
- School of Medicine, European University of Cyprus, 2404 Nicosia, Cyprus
- Correspondence:
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Delcourt T, Vanneste K, Soumali MR, Coucke W, Ghislain V, Hebrant A, Van Valckenborgh E, De Keersmaecker SCJ, Roosens NH, Van De Walle P, Van Den Bulcke M, Antoniou A. NGS for (Hemato-) Oncology in Belgium: Evaluation of Laboratory Performance and Feasibility of a National External Quality Assessment Program. Cancers (Basel) 2020; 12:E3180. [PMID: 33138022 PMCID: PMC7692129 DOI: 10.3390/cancers12113180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) is being integrated into routine clinical practice in the field of (hemato-) oncology to search for variants with diagnostic, prognostic, or therapeutic value at potentially low allelic frequencies. The complex sequencing workflows used require careful validation and continuous quality control. Participation in external quality assessments (EQA) helps laboratories evaluate their performance and guarantee the validity of tests results with the ultimate goal of ensuring high-quality patient care. Here, we describe three benchmarking trials performed during the period 2017-2018 aiming firstly at establishing the state-of-the-art and secondly setting up a NGS-specific EQA program at the national level in the field of clinical (hemato-) oncology in Belgium. DNA samples derived from cell line mixes and artificially mutated cell lines, designed to carry variants of clinical relevance occurring in solid tumors, hematological malignancies, and BRCA1/BRCA2 genes, were sent to Belgian human genetics, anatomic pathology, and clinical biology laboratories, to be processed following routine practices, together with surveys covering technical aspects of the NGS workflows. Despite the wide variety of platforms and workflows currently applied in routine clinical practice, performance was satisfactory, since participating laboratories identified the targeted variants with success rates ranging between 93.06% and 97.63% depending on the benchmark, and few false negative or repeatability issues were identified. However, variant reporting and interpretation varied, underlining the need for further standardization. Our approach showcases the feasibility of developing and implementing EQA for routine clinical practice in the field of (hemato-) oncology, while highlighting the challenges faced.
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Affiliation(s)
- Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Mohamed Rida Soumali
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Wim Coucke
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Vanessa Ghislain
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Aline Hebrant
- Cancer Centre, Sciensano, 1050 Brussels, Belgium; (A.H.); (E.V.V.); (M.V.D.B.)
| | | | - Sigrid C. J. De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Nancy H. Roosens
- Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (T.D.); (K.V.); (S.C.J.D.K.); (N.H.R.)
| | - Philippe Van De Walle
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
| | - Marc Van Den Bulcke
- Cancer Centre, Sciensano, 1050 Brussels, Belgium; (A.H.); (E.V.V.); (M.V.D.B.)
| | - Aline Antoniou
- Quality of Laboratories, Sciensano, 1050 Brussels, Belgium; (M.R.S.); (W.C.); (V.G.); (P.V.D.W.)
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28
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Prieto-Potin I, Carvajal N, Plaza-Sánchez J, Manso R, Aúz-Alexandre CL, Chamizo C, Zazo S, López-Sánchez A, Rodríguez-Pinilla SM, Camacho L, Longarón R, Bellosillo B, Somoza R, Hernández-Losa J, Fernández-Soria VM, Ramos-Ruiz R, Cristóbal I, García-Foncillas J, Rojo F. Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies. PeerJ 2020; 8:e10069. [PMID: 33083132 PMCID: PMC7546223 DOI: 10.7717/peerj.10069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/09/2020] [Indexed: 01/29/2023] Open
Abstract
Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
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Affiliation(s)
- Iván Prieto-Potin
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Nerea Carvajal
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Jenifer Plaza-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Rebeca Manso
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Carmen Laura Aúz-Alexandre
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Cristina Chamizo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Sandra Zazo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Almudena López-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | | | - Laura Camacho
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Raquel Longarón
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Rosa Somoza
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | | | - Ion Cristóbal
- Translational Oncology Division, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Jesús García-Foncillas
- Translational Oncology Division, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Federico Rojo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
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Mota A, S Oltra S, Moreno-Bueno G. Insight updating of the molecular hallmarks in ovarian carcinoma. EJC Suppl 2020; 15:16-26. [PMID: 33240439 PMCID: PMC7573468 DOI: 10.1016/j.ejcsup.2019.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/17/2019] [Accepted: 11/16/2019] [Indexed: 12/31/2022] Open
Abstract
Background and purpose Ovarian cancer (OC) is the deadliest gynaecologic cancer characterised by a high heterogeneity not only at the clinical point of view but also at the molecular level. This review focuses on the new insights about the OC molecular classification. Materials and methods We performed a bibliographic search for different indexed articles focused on the new molecular classification of OC. All of them have been published in PubMed and included information about the most frequent molecular alterations in OC confirmed by omics approaches. In addition, we have extracted information about the role of liquid biopsy in the OC diagnosis and prognosis. Results New molecular insights into OC have allowed novel clinical entities to be defined. Among OC, high-grade serous ovarian carcinoma (HGSOC) which is the most common OC is characterised by omics approaches, mutations in TP53 and in other genes involved in the homologous recombination repair, especially BRCA1/2. Recent studies in HGSOC have allowed a new molecular classification in subgroups according to their mutational, transcriptional, methylation and copy number variation signatures with a real impact in the characterisation of new therapeutic targets for OC to be defined. Furthermore, despite the intrinsic intra-tumour heterogeneity, the advances in next generation sequencing (NGS) analyses of ascetic liquid from OC have opened new ways for its characterisation and treatment. Conclusions The advances in genomic approaches have been used for the identification of new molecular profiling techniques which define OC subgroups and has supposed advances in the diagnosis and in the personalised treatment of OC. Classification of ovarian cancer regarding to widespread genetic and genomic data. Highlighted role of p53 and BRCA1/2 in ovarian cancer for diagnosis and treatment. Intra-tumour genetic heterogeneity in ovarian cancer. Useful of liquid biopsy study in ovarian cancer diagnosis.
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Affiliation(s)
- Alba Mota
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), IdiPaz, MD Anderson International Foundation Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Sara S Oltra
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), IdiPaz, MD Anderson International Foundation Madrid, Spain
| | - Gema Moreno-Bueno
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), IdiPaz, MD Anderson International Foundation Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
- Corresponding author: Departamento de Bioquímica, Facultad de Medicina (UAM), Instituto de Investigaciones Biomédicas “Alberto Sols” CSIC-UAM, Arzobispo Morcillo 4, Madrid, 28029, Spain. Fax: +34 91-5854401.
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30
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Li FX, Xie MJ, Qu SF, He D, Wu L, Liang ZK, Wu YS, Yang F, Yang XX. Detection of chromosomal abnormalities in spontaneous miscarriage by low‑coverage next‑generation sequencing. Mol Med Rep 2020; 22:1269-1276. [PMID: 32626971 PMCID: PMC7339674 DOI: 10.3892/mmr.2020.11208] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/07/2020] [Indexed: 12/21/2022] Open
Abstract
Chromosomal abnormalities (CAs) can cause spontaneous miscarriage and increase the incidence of subsequent pregnancy loss and other complications. Presently, CAs are detected mainly by array comparative genomic hybridization (CGH) and single nucleotide polymorphism microarrays. The present study developed a low‑coverage next‑generation sequencing method to detect CAs in spontaneous miscarriage and assess its clinical performance. In total, 1,401 patients who had experienced an abortion were enrolled in the present study and divided into two groups. In group I, 437 samples that had been previously validated by array CGH were used to establish a method to detect CAs using a semiconductor sequencing platform. In group II, 964 samples, which were not verified, were assessed using established methods with respect to clinical significance. Copy number variant (CNV)‑positive and euploidy samples were verified by array CGH and short tandem repeat profiling, respectively, based on quantitative fluorescent PCR. The low‑coverage sequencing method detected CNVs >1 Mb in length and a total of 3.5 million unique reads. Similar results to array CGH were obtained in group I, except for six CNVs <1 Mb long. In group II, there were 341 aneuploidies, 195 CNVs, 25 mosaicisms and 403 euploidies. Overall, among the 1,401 abortion samples, there were 536 aneuploidies, 263 CNVs, 34 mosaicisms, and 568 euploidies. Trisomies were present in all autosomal chromosomes. The most common aneuploidies were T16, monosomy X, T22, T15, T21 and T13. Furthermore, one tetrasomy 21, one CNV associated with Wolf‑Hirschhorn syndrome, one associated with DiGeorge syndrome and one associated with both Prader‑Willi and Angelman syndromes were identified. These four cases were confirmed by short tandem repeat profiling and array CGH. Quantitative fluorescent PCR revealed nine polyploidy samples. The present method demonstrated equivalent efficacy to that of array CGH in detecting CNVs >1 Mb, with advantages of requiring less input DNA and lower cost.
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Affiliation(s)
- Fen-Xia Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Mei-Juan Xie
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Shou-Fang Qu
- National Institutes for Food and Drug Control, Beijing 100050, P.R. China
| | - Dan He
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong 510665, P.R. China
| | - Long Wu
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong 510665, P.R. China
| | - Zhi-Kun Liang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong 510665, P.R. China
| | - Ying-Song Wu
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fang Yang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xue-Xi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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Standardization of Somatic Variant Classifications in Solid and Haematological Tumours by a Two-Level Approach of Biological and Clinical Classes: An Initiative of the Belgian ComPerMed Expert Panel. Cancers (Basel) 2019; 11:cancers11122030. [PMID: 31888289 PMCID: PMC6966529 DOI: 10.3390/cancers11122030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
In most diagnostic laboratories, targeted next-generation sequencing (NGS) is currently the default assay for the detection of somatic variants in solid as well as haematological tumours. Independent of the method, the final outcome is a list of variants that differ from the human genome reference sequence of which some may relate to the establishment of the tumour in the patient. A critical point towards a uniform patient management is the assignment of the biological contribution of each variant to the malignancy and its subsequent clinical impact in a specific malignancy. These so-called biological and clinical classifications of somatic variants are currently not standardized and are vastly dependent on the subjective analysis of each laboratory. This subjectivity can thus result in a different classification and subsequent clinical interpretation of the same variant. Therefore, the ComPerMed panel of Belgian experts in cancer diagnostics set up a working group with the goal to harmonize the biological classification and clinical interpretation of somatic variants detected by NGS. This effort resulted in the establishment of a uniform, two-level classification workflow system that should enable high consistency in diagnosis, prognosis, treatment and follow-up of cancer patients. Variants are first classified into a tumour-independent biological five class system and subsequently in a four tier ACMG clinical classification. Here, we describe the ComPerMed workflow in detail including examples for each step of the pipeline. Moreover, this workflow can be implemented in variant classification software tools enabling automatic reporting of NGS data, independent of panel, method or analysis software.
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32
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Gullapalli RR. Evaluation of Commercial Next-Generation Sequencing Bioinformatics Software Solutions. J Mol Diagn 2019; 22:147-158. [PMID: 31751676 DOI: 10.1016/j.jmoldx.2019.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) diagnostics continue to expand rapidly in clinical medicine. An ever-expanding menu of molecular biomarkers is deemed important for diagnostic, prognostic, and therapeutic assessment in patients. The increasing role of NGS in the clinic is driven mainly by the falling costs of sequencing. However, the data-intensive nature of NGS makes bioinformatic analysis a major challenge to many clinical laboratories. Critically needed NGS bioinformatics personnel are hard to recruit and retain in small- to mid-size clinical laboratories. Also, NGS software often lacks the scalability necessary for expanded clinical laboratory testing volumes. Commercial software solutions aim to bridge the bioinformatics barrier via turnkey informatics solutions tailored specifically for the clinical workplace. Yet, there has been no systematic assessment of these software solutions thus far. This article presents an end-to-end vendor evaluation experience of commercial NGS bioinformatics solutions. Six different commercial vendor solutions were assessed systematically. Key metrics of NGS software evaluation to aid in the robust assessment of software solutions are described. Comprehensive feedback, provided by the TriCore Reference Laboratories molecular pathology team, enabled the final vendor selection. Many key lessons were learned during the software evaluation process, which are described herein. This article aims to provide a detailed road map for small- to mid-size clinical laboratories interested in evaluating commercial bioinformatics solutions available in the marketplace.
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Affiliation(s)
- Rama R Gullapalli
- Departments of Pathology and Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico.
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Lv P, Yang S, Liu W, Qin H, Tang X, Wu F, Liu Z, Gao H, Liu X. Circulating plasma lncRNAs as novel markers of EGFR mutation status and monitors of epidermal growth factor receptor-tyrosine kinase inhibitor therapy. Thorac Cancer 2019; 11:29-40. [PMID: 31691525 PMCID: PMC6938758 DOI: 10.1111/1759-7714.13216] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022] Open
Abstract
Background Epidermal growth factor receptor (EGFR) gene mutations predict tumor response to EGFR tyrosine kinase inhibitors (EGFR‐TKIs) in non‐small cell lung cancer (NSCLC). However, even patients with EGFR‐sensitive mutations in NSCLC have limited efficacy with EGFR‐TKI. Studies have shown that long noncoding RNA (lncRNA) is related to diagnosis and prognosis with NSCLC. This study aimed to explore the correlation between lncRNA in NSCLC patients with EGFR mutation status and EGFR‐TKI efficacy. Methods The amplification‐refractory mutation system method was used to test the EGFR mutation status in tumor tissues and pleural effusions of NSCLC patients. Three EGFR‐mutant patients and three EGFR wild‐type patients were selected. Differential lncRNA was performed on the pleural effusions of the two selected groups of patients using Clariom D Human chip technology. Five lncRNAs significantly associated with EGFR mutation status were screened by FC value and GO analysis, and then evaluated by real‐time quantitative polymerase chain reaction in NSCLC patients' pleural effusions. Three were further analyzed in NSCLC patients' plasma. Results There were 61 significant differences in lncRNA between EGFR mutation‐positive and wild‐type patients. Among them, SCARNA7, MALAT1, NONHSAT017369, NONHSAT051892, and FTH1P2 were significantly associated with EGFR mutation status. SCARNA7, MALAT1, and NONHSAT017369 showed consistent results with plasma in pleural effusions compared to EGFR wild‐type, all upregulated in the EGFR mutation group. Conclusion This study shows that lncRNAs can be used not only as potential biomarkers for predicting the mutation status of EGFR and the efficacy of EGFR‐TKI, but also for monitoring the efficacy of EGFR‐TKI.
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Affiliation(s)
- Panpan Lv
- Academy of Military Medical Science, Beijing, China.,PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shaoxing Yang
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Wenjing Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Haifeng Qin
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xiuhua Tang
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Wu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Zeyuan Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Hongjun Gao
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xiaoqing Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
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Mapping the Mutation Landscape of Colorectal Cancer. Am J Med Sci 2019; 358:313-314. [PMID: 31655711 DOI: 10.1016/j.amjms.2019.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]
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Kim JY, Byeon JS. Genetic Counseling and Surveillance Focused on Lynch Syndrome. JOURNAL OF THE ANUS RECTUM AND COLON 2019; 3:60-68. [PMID: 31559369 PMCID: PMC6752118 DOI: 10.23922/jarc.2019-002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
Lynch syndrome is a hereditary cancer syndrome caused by germline mutations in one of several DNA mismatch repair genes. Lynch syndrome leads to an increased lifetime risk of various cancers, particularly colorectal, and endometrial cancers. After identifying patients suspected of having Lynch syndrome by clinical criteria, computational prediction models, and/or universal tumor testing, genetic testing is performed to confirm the diagnosis. Before and after genetic testing, genetic counseling should be provided. Genetic counseling should involve a detailed personal and family history, information on the disorder and genetic tests, discussion of the management and surveillance of the disease, career plan, family plan, and psychosocial support. Surveillance of colorectal cancer and other malignancies is of paramount importance for properly managing Lynch syndrome. This review focuses on important considerations in genetic counseling and the latest insights into the surveillance of individuals and families with Lynch syndrome.
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Affiliation(s)
- Jin Yong Kim
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jeong-Sik Byeon
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Thiemeyer H, Taher L, Schille JT, Harder L, Hungerbuehler SO, Mischke R, Hewicker-Trautwein M, Kiełbowicz Z, Brenig B, Schütz E, Beck J, Murua Escobar H, Nolte I. Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate. Sci Rep 2019; 9:13216. [PMID: 31519932 PMCID: PMC6744464 DOI: 10.1038/s41598-019-49271-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-Seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.
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Affiliation(s)
- H Thiemeyer
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - J T Schille
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - L Harder
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - S O Hungerbuehler
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - R Mischke
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - M Hewicker-Trautwein
- Institute of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Z Kiełbowicz
- Department and Clinic of Veterinary Surgery, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - B Brenig
- University of Göttingen, Institute of Veterinary Medicine, Göttingen, Germany
| | - E Schütz
- Chronix Biomedical, Göttingen, Germany
| | - J Beck
- Chronix Biomedical, Göttingen, Germany
| | - H Murua Escobar
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Department of Haematology/Oncology/Palliative Care, Rostock University Medical Centre, Rostock, Germany
| | - I Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.
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Gabaldón T. Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev 2019; 43:517-547. [PMID: 31158289 PMCID: PMC8038933 DOI: 10.1093/femsre/fuz015] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/31/2019] [Indexed: 12/29/2022] Open
Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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Liu N, Kan J, Cao W, Cao J, Jiang E, Zhou Y, Zhao M, Feng J. Metagenomic next-generation sequencing diagnosis of peripheral pulmonary infectious lesions through virtual navigation, radial EBUS, ultrathin bronchoscopy, and ROSE. J Int Med Res 2019; 47:4878-4885. [PMID: 31436107 PMCID: PMC6833387 DOI: 10.1177/0300060519866953] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Objective To evaluate the efficacy of combined rapid on-site evaluation of cytology (ROSE), ultrathin bronchoscopy, virtual bronchoscopic navigation, radial endobronchial ultrasound (EBUS), and metagenomic next-generation sequencing (mNGS) for diagnosis of peripheral pulmonary infectious lesions. Methods Specimens from patients with peripheral lung infection were obtained by transbronchial lung biopsy (TBLB) and bronchoalveolar lavage (BAL), and mNGS was used to detect pathogenic microorganisms. The sensitivity and specificity of mNGS were compared between TBLB tissue and BAL fluid. Results The most common pathogens of pulmonary infectious lesions in this study were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. The specificity of mNGS was higher in TBLB tissue than in BAL fluid, but mNGS of BAL fluid had higher sensitivity. Conclusions The combination of ROSE, ultrathin bronchoscopy, virtual bronchoscopic navigation, radial EBUS, and mNGS technology yielded high efficacy for the diagnosis of peripheral pulmonary infectious lesions. TBLB and BAL specimens have respective advantages in specificity and sensitivity for mNGS analysis.
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Affiliation(s)
- Nana Liu
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China
- Department of Critical Care Medicine, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Jianying Kan
- Department of Critical Care Medicine, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, China
| | - Wenbin Cao
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jie Cao
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Erlie Jiang
- Hematopoietic Stem Cell Transplantation Center, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yang Zhou
- Department of Pathology, BGI-Shanghai, Shanghai, China
| | - Mingfeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Jing Feng
- Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China
- Jing Feng, Department of Respiratory, Tianjin Medical University General Hospital, Tianjin, China. No. 154 Anshan Road, Tianjin 300052, China.
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New Era of Endoscopic Ultrasound-Guided Tissue Acquisition: Next-Generation Sequencing by Endoscopic Ultrasound-Guided Sampling for Pancreatic Cancer. J Clin Med 2019; 8:jcm8081173. [PMID: 31387310 PMCID: PMC6723875 DOI: 10.3390/jcm8081173] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/20/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022] Open
Abstract
Pancreatic cancer is a lethal cancer with an increasing incidence. Despite improvements in chemotherapy, patients with pancreatic cancer continue to face poor prognoses. Endoscopic ultrasound-guided tissue acquisition (EUS-TA) is the primary method for obtaining tissue samples of pancreatic cancer. Due to advancements in next-generation sequencing (NGS) technologies, multiple parallel sequencing can be applied to EUS-TA samples. Genomic biomarkers for therapeutic stratification in pancreatic cancer are still lacking, however, NGS can unveil potential predictive genomic biomarkers of treatment response. Thus, the importance of NGS using EUS-TA samples is becoming recognized. In this review, we discuss the recent advances in EUS-TA application for NGS of pancreatic cancer.
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Parker JDK, Yap SQ, Starks E, Slind J, Swanson L, Docking TR, Fuller M, Zhou C, Walker B, Filipenko D, Xiong W, Karimuddin AA, Phang PT, Raval M, Brown CJ, Karsan A. Fixation Effects on Variant Calling in a Clinical Resequencing Panel. J Mol Diagn 2019; 21:705-717. [PMID: 31055024 DOI: 10.1016/j.jmoldx.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 11/16/2022] Open
Abstract
Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review.
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Affiliation(s)
- Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Shyong Quin Yap
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Elizabeth Starks
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jillian Slind
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Lucas Swanson
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - T Roderick Docking
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chen Zhou
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair Walker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Douglas Filipenko
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Wei Xiong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Ahmer A Karimuddin
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - P Terry Phang
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Manoj Raval
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Carl J Brown
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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Otsubo K, Sakai K, Takeshita M, Harada D, Azuma K, Ota K, Akamatsu H, Goto K, Horiike A, Kurata T, Nakagaki N, Nosaki K, Iwama E, Nakanishi Y, Nishio K, Okamoto I. Genetic Profiling of Non-Small Cell Lung Cancer at Development of Resistance to First- or Second-Generation EGFR-TKIs by CAPP-Seq Analysis of Circulating Tumor DNA. Oncologist 2019; 24:1022-1026. [PMID: 31023862 DOI: 10.1634/theoncologist.2019-0101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/28/2019] [Indexed: 01/16/2023] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) treated with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) eventually acquire resistance to these drugs. The identification of various resistance mechanisms for determination of subsequent treatment for these patients will require a method for simultaneous detection of multiple genetic alterations with high sensitivity. We performed cancer personalized profiling by deep sequencing (CAPP-Seq) with circulating tumor DNA obtained from patients with NSCLC who acquired resistance to first- or second-generation EGFR-TKIs. Plasma samples from 27 patients were analyzed, and 24 samples underwent CAPP-Seq successfully. Original activating EGFR mutations were detected in 23 patients, with the remaining patient showing MET amplification. With regard to known mechanisms of EGFR-TKI resistance, the T790M mutation of EGFR was detected in 17 of the 24 patients, MET amplification in 9 patients (6 of whom also harbored T790M), ERBB2 amplification in 2 patients (1 of whom also harbored T790M), and EGFR amplification in 4 patients (all of whom harbored T790M). Our results thus show that CAPP-Seq is applicable to clinical samples for the identification of multiple somatic mutations in circulating tumor DNA obtained from patients with NSCLC at the time of disease progression during treatment with first- or second-generation EGFR-TKIs. Patients positive for the T790M mutation of EGFR were also found to constitute a molecularly heterogeneous population. KEY POINTS: CAPP-Seq is applicable to clinical samples for the identification of multiple somatic mutations.The T790M mutation of EGFR is associated with amplification of MET, ERBB2, or EGFR in NSCLC patients resistant to EGFR-TKIs.T790M-positive patients are molecularly heterogeneous, and genetic alterations coexisting with T790M may differ between patients treated with first-generation or second-generation EGFR-TKIs.
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Affiliation(s)
- Kohei Otsubo
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Masafumi Takeshita
- Department of Respiratory Medicine, Kitakyushu Municipal Medical Center, Kitakyushu, Japan
| | - Daijiro Harada
- Department of Thoracic Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama, Japan
| | - Koichi Azuma
- Division of Respirology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Keiichi Ota
- Division of Respiratory Medicine, National Hospital Organization Fukuoka-Higashi Medical Center, Koga, Fukuoka, Japan
| | - Hiroaki Akamatsu
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Atsushi Horiike
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takayasu Kurata
- Department of Thoracic Oncology, Kansai Medical University Hospital, Hirakata, Osaka, Japan
| | - Noriaki Nakagaki
- Department of Respiratory Medicine, Steel Memorial Yawata Hospital, Kitakyushu, Japan
| | - Kaname Nosaki
- Department of Thoracic Oncology, National Kyushu Cancer Center, Fukuoka, Japan
| | - Eiji Iwama
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoichi Nakanishi
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Isamu Okamoto
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Toth LN, Green D, Peterson J, Deharvengt SJ, de Abreu FB, Loo EY. Variant allele frequencies do not correlate well with myeloblast counts in a clinically validated gene sequencing panel for routine acute myeloid leukemia workup. Leuk Lymphoma 2019; 60:2415-2422. [DOI: 10.1080/10428194.2019.1587757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Laura N. Toth
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Donald Green
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Jason Peterson
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Sophie J. Deharvengt
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Francine B. de Abreu
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
| | - Eric Y. Loo
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center One Medical Center Drive, Lebanon, NH, USA
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Alonso CM, Llop M, Sargas C, Pedrola L, Panadero J, Hervás D, Cervera J, Such E, Ibáñez M, Ayala R, Martínez-López J, Onecha E, de Juan I, Palanca S, Martínez-Cuadrón D, Rodríguez-Veiga R, Boluda B, Montesinos P, Sanz G, Sanz MA, Barragán E. Clinical Utility of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia Diagnostics. J Mol Diagn 2019; 21:228-240. [DOI: 10.1016/j.jmoldx.2018.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 09/06/2018] [Accepted: 09/20/2018] [Indexed: 10/27/2022] Open
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Guerini-Rocco E, Passaro A, Casadio C, De Luca VM, Guarize J, de Marinis F, Vacirca D, Barberis M. Acquired Resistance to Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancers: The Role of Next-Generation Sequencing on Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples. Arch Pathol Lab Med 2019; 142:465-473. [PMID: 29565206 DOI: 10.5858/arpa.2017-0158-ra] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Molecular testing is essential for the diagnostic workup of patients with advanced non-small cell lung cancers. Cytology specimens from minimally invasive procedures, such as endobronchial ultrasound-guided transbronchial needle aspiration, are often the only available samples for these patients. The implementation of molecular diagnostic testing, and in particular next-generation sequencing-based testing, on these cytologic specimens is currently an evolving field for lung cytopathology. The application of these molecular analyses on tyrosine kinase inhibitor-resistant non-small cell lung cancers raises unique technical, biologic, and clinical challenges. OBJECTIVE - To provide an overview of the implementation of next-generation sequencing analysis on endobronchial ultrasound-guided transbronchial needle aspiration samples to detect the molecular aberrations underneath the phenomenon of acquired resistance in patients with non-small cell lung cancers progressing while on the EGFR/ALK tyrosine kinase inhibitor treatment. DATA SOURCES - Peer-reviewed original articles, review articles, and published guidelines and expert opinion reports were reviewed, together with our single-center experience. CONCLUSIONS - Next-generation sequencing analyses and the endobronchial ultrasound-guided transbronchial needle aspiration procedure may represent a valuable strategy to address the unique requirements of molecular testing on tyrosine kinase inhibitor-resistant non-small cell lung cancers.
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Affiliation(s)
| | | | | | | | | | | | | | - Massimo Barberis
- From the Divisions of Pathology (Drs Guerini-Rocco, Casadio, Midolo De Luca, and Barberis, and Mr Vacirca), Thoracic Oncology (Drs Passaro and de Marinis), and Thoracic Surgery (Dr Guarize), European Institute of Oncology, Milan, Italy
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Zhang X, Liang Z, Wang S, Lu S, Song Y, Cheng Y, Ying J, Liu W, Hou Y, Li Y, Liu Y, Hou J, Liu X, Shao J, Tai Y, Wang Z, Fu L, Li H, Zhou X, Bai H, Wang M, Lu Y, Yang J, Zhong W, Zhou Q, Yang X, Wang J, Huang C, Liu X, Zhou X, Zhang S, Tian H, Chen Y, Ren R, Liao N, Wu C, Zhu Z, Pan H, Gu Y, Wang L, Liu Y, Zhang S, Liu T, Chen G, Shao Z, Xu B, Zhang Q, Xu R, Shen L, Wu Y, Tumor Biomarker Committee OBOCSOCO(CSCO. Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology. Cancer Biol Med 2019; 16:189-204. [PMID: 31119060 PMCID: PMC6528448 DOI: 10.20892/j.issn.2095-3941.2018.0142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/20/2018] [Indexed: 02/05/2023] Open
Abstract
Next-generation sequencing (NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously. Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology (CSCO) and the China Actionable Genome Consortium (CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians, pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure (SOP), data analysis, report, and NGS platform certification and validation.
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Affiliation(s)
- Xuchao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Shengyue Wang
- National Research Center for Translational Medicine, Shanghai, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Song
- Division of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210029, China
| | - Ying Cheng
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 519000, China
| | - Yi Liu
- Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Hou
- Department of Oncology, First Clinical College of South China University of Technology/Guangdong Lung Cancer Institute, Guangzhou 510060, China
| | - Xiufeng Liu
- People's Liberation Army Cancer Center of Bayi Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Jianyong Shao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Yanhong Tai
- Department of Pathology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Zheng Wang
- Department of Pathology, Beijing Hospital, Beijing 100071, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory of Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hui Li
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Xiaojun Zhou
- Department of Pathology, Jinling Hospital Nanjing University School of Medicine, Nanjing 210029, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Mengzhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - You Lu
- Department of Oncology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Jinji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenzhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xuening Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Cheng Huang
- Department of Thoracic Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350001, China
| | - Xiaoqing Liu
- Department of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiaoyan Zhou
- Department of Pathology, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Shirong Zhang
- Center for Translational Medicine, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Hongxia Tian
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Yu Chen
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Ruibao Ren
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangzhou 510080, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200240, China
| | - Zhongzheng Zhu
- Department of Oncology, No. 113 Hospital of People's Liberation Army, Ningbo 315040, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China
| | - Liwei Wang
- Department of Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110016, China
| | - Suzhan Zhang
- Department of Oncology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Tianshu Liu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Gong Chen
- Department of Colorectal, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Zhimin Shao
- Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Qingyuan Zhang
- Department of Internal Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin 150030, China
| | - Ruihua Xu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 519000, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yilong Wu
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
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Hovhannisyan H, Gabaldón T. Transcriptome Sequencing Approaches to Elucidate Host-Microbe Interactions in Opportunistic Human Fungal Pathogens. Curr Top Microbiol Immunol 2019; 422:193-235. [PMID: 30128828 DOI: 10.1007/82_2018_122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Infections caused by opportunistic human fungal pathogens are a source of increasing medical concern, due to their growing incidence, the emergence of novel pathogenic species, and the lack of effective diagnostics tools. Fungal pathogens are phylogenetically diverse, and their virulence mechanisms can differ widely across species. Despite extensive efforts, the molecular bases of virulence in pathogenic fungi and their interactions with the human host remain poorly understood for most species. In this context, next-generation sequencing approaches hold the promise of helping to close this knowledge gap. In particular, high-throughput transcriptome sequencing (RNA-Seq) enables monitoring the transcriptional profile of both host and microbes to elucidate their interactions and discover molecular mechanisms of virulence and host defense. Here, we provide an overview of transcriptome sequencing techniques and approaches, and survey their application in studying the interplay between humans and fungal pathogens. Finally, we discuss novel RNA-Seq approaches in studying host-pathogen interactions and their potential role in advancing the clinical diagnostics of fungal infections.
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Affiliation(s)
- Hrant Hovhannisyan
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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Abstract
Large-scale tumor profiling studies have generated massive amounts of data that have been instrumental for the detection of recurrent driver mutations in many tumor types. These driver mutations as well as the concurrent passenger mutations are now being used for a more accurate diagnosis of the tumor and prognosis for the patient. Moreover, therapeutic inhibitors toward specific mutations are already on the market and many clinical trials are ongoing to approve novel therapeutic drugs. The broad-range identification of these somatic mutations is key to this tailored personalized medicine approach, which preferentially has to be performed by a multigene multihotspot method such as massive parallel sequencing, also called next generation sequencing (NGS). The implementation of NGS in molecular diagnostics of tumor profiling however, requires a firm validation to minimize the occurrence of false positives and false negatives, thereby yielding highly accurate and robust clinical data.Here, we describe the different performance characteristics as well as quality metrics that should be analyzed for the robust diagnostic validation of tumor profiling in order to meet the requirements of international standards specific for medical laboratories, such as the ISO15189:2012 standard. These metrics include assays that assess the precision, limit of detection, accuracy, sensitivity, specificity, and robustness of the entire workflow from DNA enrichment up to the final report.
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Affiliation(s)
- Guy Froyen
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - Brigitte Maes
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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Prospective multicenter real-world RAS mutation comparison between OncoBEAM-based liquid biopsy and tissue analysis in metastatic colorectal cancer. Br J Cancer 2018; 119:1464-1470. [PMID: 30467411 PMCID: PMC6288144 DOI: 10.1038/s41416-018-0293-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023] Open
Abstract
Background Liquid biopsy offers a minimally invasive alternative to tissue-based evaluation of mutational status in cancer. The goal of the present study was to evaluate the aggregate performance of OncoBEAM RAS mutation analysis in plasma of colorectal cancer (CRC) patients at 10 hospital laboratories in Spain where this technology is routinely implemented. Methods Circulating cell-free DNA from plasma was examined for RAS mutations using the OncoBEAM platform at each hospital laboratory. Results were then compared to those obtained from DNA extracted from tumour tissue from the same patient. Results The overall percentage agreement between plasma-based and tissue-based RAS mutation testing of the 236 participants was 89% (210/236; kappa, 0.770 (95% CI: 0.689–0.852)). Re-analysis of tissue from all discordant cases by BEAMing revealed two false negative and five false positive tumour tissue RAS results, with a final concordance of 92%. Plasma false negative results were found more frequently in patients with exclusive lung metastatic disease. Conclusions In this first prospective real-world RAS mutation performance comparison study, a high overall agreement was observed between results obtained from plasma and tissue samples. Overall, these findings indicate that the plasma-based BEAMing assay is a viable solution for rapid delivery of RAS mutation status to determine mCRC patient eligibility for anti-EGFR therapy.
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Chen H, Luthra R, Patel KP, Routbort M, Rashid A, Roy-Chowdhuri S, Lazar A, Broaddus R, Manekia J, Singh RR, Yemelyanova A. Challenges in next generation sequencing analysis of somatic mutations in transplant patients. Cancer Genet 2018; 226-227:17-22. [DOI: 10.1016/j.cancergen.2018.04.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/16/2018] [Accepted: 04/26/2018] [Indexed: 10/16/2022]
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Inadequate Rates of BRCA Testing with its Negative Consequences for Women with Epithelial Ovarian Cancer and their Families: an Overview of the Literature. Clin Oncol (R Coll Radiol) 2018; 30:472-483. [DOI: 10.1016/j.clon.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/18/2018] [Indexed: 12/19/2022]
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